PureCN

PureCN estimates allele-specific copy number, tumor purity, loss of heterozygosity, and classifies somatic versus germline single nucleotide variants from tumor sequencing data.

Key Features:

• Tumor Purity Estimation: Estimates tumor purity by analyzing allelic fractions to distinguish somatic and germline variants.
• Copy Number Analysis: Provides estimation of copy number variations (CNVs) with allele-specific copy number calls relevant to cancer genomics.
• Loss of Heterozygosity (LOH): Detects LOH events to identify genomic regions with lost heterozygosity due to tumor progression.
• Single Nucleotide Variant (SNV) Classification: Classifies SNVs by somatic status and clonality, distinguishing germline mutations from somatic alterations.

Scientific Applications:

• Retrospective Exploratory Analyses: Classifies variants of uncertain significance (VUS) as somatic or germline in retrospective studies.
• Molecular Diagnostics: Supports tumor-only sequencing assays to identify known somatic alterations in cancer genes for diagnostic evaluation.

Methodology:

Leverages differences in expected allelic fractions between germline and somatic variants caused by contamination with normal cells and adjusts for local copy number variations to infer genotypes.